Official figures show the overall pass rate at Higher has risen by one percentage point to a record 93%, while the proportion of exams passed at A grade has climbed to 56%.
The increase in A grades is particularly marked, with a nine percentage point rise since 2007.
The pass rate for Advanced Highers has also increased by one percentage point to 92%, with half of exams sat now resulting in A grades.
However, there has been a decline in the number of pupils taking the Government's new Scottish Baccalaureate exams, with only seven entries this year, compared to 15 in 2011.
The Scottish Government devised the baccalaureates to encourage more pupils to study science and languages, but private schools have expressed concern they are not recognised by universities.
The best performing school at Higher was the small St Mary's Music School, in Edinburgh, which had a 100% pass rate, but only 11 pupils sitting Highers this year.
Of the larger schools, Mary Erskine, a girls' school in Edinburgh, came top with a pass rate of 97.7%, closely followed by the High School of Glasgow, with a pass rate of 97.5%.
David Gray, principal of Mary Erskine, which charges £9366 a year for a senior school day pupil, said the single-sex status of the school helped maintain results.
He added: "I am delighted the pupils have performed so well. We find the single sex, academic environment during the adolescent years helps them to focus and allows them to flourish across the academic spectrum,"
Colin Mair, rector of Glasgow High School, which charges £10,236 a year, said the school worked hard to maximise the potential of all pupils.
He said: "All pupils are achieving success in relation to their individual targets, not just the most able. We believe also that all these senior pupils have benefited from keen participation in a wide range of cultural, sporting and extra-curricular activities."
The private school exam results compare with a national Higher pass rate for all Scottish schools of 77%.
However, most private schools select their pupils on the basis of their ability, while state schools teach children of all abilities.
John Edward, director of the Scottish Council of Independent Schools (SCIS), which compiled the results, praised the sector.
He said: "These examination results, combined with those at A-level and the International Baccalaureate, are a timely reminder of the core academic abilities nurtured in independent schools. Over half of all Advanced Highers, Highers, Standard Grades and Scottish Baccalaureates sat by pupils in the independent sector this year were awarded grade A.
"That's a gold medal achievement by pupils and confirmation of the quality of teaching that exists in the sector."
Of the schools that study A levels, Merchiston Castle, in Edinburgh, came top with a pass rate of 96.2%.
On Saturday, The Herald revealed that Scottish private schools had increased their fees for the new term by more than the rate of inflation, bringing the average cost to more than £12,000 a year for the first time.
The survey found the cost to parents of sending their children to an independent school has risen by 3.5% in 2012/13 – with the highest fees topping £21,000.
Many schools have kept fee rises low, but the increase will put pressure on parents coping with the recession – particularly those for whom private education is at the limits of affordability.
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